def test_h5tonc(self):
"""check h5 <--> netCDF conversion"""
self.filenc = tempfile.mktemp(".nc")
self.fileh5 = tempfile.mktemp(".h5")
# convert to netCDF
f = NetCDF.NetCDFFile(self.file)
f.h5tonc(self.filenc)
f.close()
# convert back to HDF5
f = NetCDF.NetCDFFile(self.fileh5, 'w')
nobjects, nbytes = f.nctoh5(self.filenc)
# check to see that correct number of objects and bytes converted.
assert (nobjects, nbytes) == (5, 529)
# check that __repr__() on new HDF5 file is same as original
outstring = "%s {\ndimensions:\n lat = 3 ;\n lon = 7 ;\n t = UNLIMITED ; // (4 currently)\n nchar = 2 ;\nvariables:\n byte lat('lat',) ;\n lat:units = 'degrees north' ;\n character lon('nchar', 'lon') ;\n lon:units = 'degrees east' ;\n float foo('t', 'lat', 'lon') ;\n foo:missing_value = -999 ;\n foo:units = 'Watts' ;\n double bar('lat', 'lon') ;\n bar:missing_value = -999 ;\n bar:units = 'Ergs' ;\n short time('t',) ;\n time:units = 'Years' ;\n// global attributes:\n :history = 'created today' ;\n :magicNumbers = [42.0, 3.145, -1.0] ;\n :title = 'unit test' ;\n}" % self.fileh5
assert f.__repr__() == outstring
f.close()
# check that size of new HDF5 file is same as original
# (not a good idea, filesizes should not be expected to be the same)
# file1size = os.stat(self.file).st_size
# file2size = os.stat(self.fileh5).st_size
# if common.verbose:
# print "file1size-->", file1size
# print "file2size-->", file2size
# assert file1size == file2size
os.remove(self.filenc)
os.remove(self.fileh5)
def test_dimensions(self):
"""check dimensions names and sizes"""
f = NetCDF.NetCDFFile(self.file)
dims = f.dimensions
assert dims == {'lat': 3, 'lon': 7, 'nchar': 2, 't': None}
f.close()
def test_repr(self):
"""open file and examine the __repr__ method"""
f = NetCDF.NetCDFFile(self.file)
outstring = "%s {\ndimensions:\n lat = 3 ;\n lon = 7 ;\n t = UNLIMITED ; // (4 currently)\n nchar = 2 ;\nvariables:\n byte lat('lat',) ;\n lat:units = 'degrees north' ;\n character lon('nchar', 'lon') ;\n lon:units = 'degrees east' ;\n float foo('t', 'lat', 'lon') ;\n foo:missing_value = -999 ;\n foo:units = 'Watts' ;\n double bar('lat', 'lon') ;\n bar:missing_value = -999 ;\n bar:units = 'Ergs' ;\n short time('t',) ;\n time:units = 'Years' ;\n// global attributes:\n :history = 'created today' ;\n :magicNumbers = [42.0, 3.145, -1.0] ;\n :title = 'unit test' ;\n}" % self.file
assert f.__repr__() == outstring
f.close()
def test_fileattrs(self):
"""check global attributes"""
f = NetCDF.NetCDFFile(self.file)
fileattrs = f.ncattrs()
assert fileattrs == ['history', 'magicNumbers', 'title']
assert f.history == 'created today'
assert f.magicNumbers == [42.0, 3.145, -1.0]
assert f.title == 'unit test'
f.close()
def test_appendata(self):
"""test appending data to an existing file"""
f = NetCDF.NetCDFFile(self.file, 'a')
timedata = f.variables['time']
timedata[3] = 40.
timedata.append(50.)
self.timedata = timedata[:]
f.close()
# close the file, re-open it
f = NetCDF.NetCDFFile(self.file)
timedata = f.variables['time']
# check that data was actually appended
assert timedata.shape == (5, )
assert timedata[:].tolist() == self.timedata.tolist()
# make sure that foo now contains _FillValue at the end of unlim dim
foodata = f.variables['foo']
assert foodata[-1, -1, -1] > 9.9 + 36
f.close()
def setUp(self):
# Create an HDF5 with the NetCDF interface.
self.file = tempfile.mktemp(".h5")
file = NetCDF.NetCDFFile(self.file, mode="w", history="created today")
# create some dimensions.
file.createDimension('t', None)
file.createDimension('lat', 3)
file.createDimension('lon', 7)
file.createDimension('nchar', 2)
# create some variables.
# foo has an unlimited dimension
foo = file.createVariable('foo', 'f', ('t', 'lat', 'lon'))
# bar does not
bar = file.createVariable('bar', 'd', ('lat', 'lon'))
# coordinate variables.
times = file.createVariable('time', 's', ('t', ))
lats = file.createVariable('lat', '1', ('lat', ))
lons = file.createVariable('lon', 'c', ('nchar', 'lon'))
# add some data.
self.latdata = numpy.arange(100, 400, 100, dtype='int8')
lats[:] = self.latdata
self.londata = [['a', 'b', 'c', 'd', 'e', 'f', 'g'],
['a', 'b', 'c', 'd', 'e', 'f', 'g']]
lons[:] = self.londata
for i in numpy.arange(bar.shape[0]):
for j in numpy.arange(bar.shape[1]):
bar[i, j] = i * j
self.bardata = bar[:]
# append data along unlimited dimension.
nmax = 4
for n in range(nmax):
foo.append(n * numpy.ones(bar.shape, 'f'))
if n != nmax - 1: # don't fill in last time
times.append(10 * (n + 1))
file.sync() # fill in timedata with _FillValue
self.timedata = times[:]
self.foodata = foo[:]
# some file attributes
file.title = 'unit test'
file.magicNumbers = [42., 3.145, -1.]
# some variable attributes
bar.units = 'Ergs'
bar.missing_value = -999
foo.units = 'Watts'
foo.missing_value = -999
times.units = 'Years'
lats.units = 'degrees north'
lons.units = 'degrees east'
file.close()
def test_variabledata(self):
"""check data in variables"""
f = NetCDF.NetCDFFile(self.file)
latdata = f.variables['lat'][:]
londata = f.variables['lon'][:]
foodata = f.variables['foo'][:]
bardata = f.variables['bar'][:]
timedata = f.variables['time'][:]
assert latdata.tolist() == self.latdata.tolist()
assert londata.tolist() == self.londata
assert foodata.tolist() == self.foodata.tolist()
assert bardata.tolist() == self.bardata.tolist()
assert timedata.tolist() == self.timedata.tolist()
f.close()
def test_varttrs(self):
"""check variable names and variable attributes"""
f = NetCDF.NetCDFFile(self.file)
vars = f.variables.keys()
assert vars == ['lat', 'lon', 'foo', 'bar', 'time']
lats = f.variables['lat']
assert lats.units == 'degrees north'
lons = f.variables['lon']
assert lons.units == 'degrees east'
times = f.variables['time']
assert times.units == 'Years'
foo = f.variables['foo']
assert foo.units == 'Watts'
assert foo.missing_value == -999
bar = f.variables['bar']
assert bar.units == 'Ergs'
assert bar.missing_value == -999
f.close()
# first, use Scientific.IO.NetCDF
t1 = time.time()
file = Scientific.IO.NetCDF.NetCDFFile('test.nc', 'w')
file.createDimension('n1', None)
file.createDimension('n2', n2dim)
foo = file.createVariable('data', 'd', (
'n1',
'n2',
))
for n in range(n1dim):
foo[n] = array[n]
file.close()
print 'Scientific.IO.NetCDF took', time.time() - t1, 'seconds'
# now use pytables NetCDF emulation layer.
t1 = time.time()
file = NetCDF.NetCDFFile('test.h5', 'w')
file.createDimension('n1', None)
file.createDimension('n2', n2dim)
# no compression (override default filters instance).
foo = file.createVariable('data', 'd', (
'n1',
'n2',
), filters=filters)
# this is faster
foo.append(array)
file.close()
print 'pytables NetCDF (1) took', time.time() - t1, 'seconds'
t1 = time.time()
file = NetCDF.NetCDFFile('test.h5', 'w')
file.createDimension('n1', None)
file.createDimension('n2', n2dim)
### bogus example to illustrate the use of tables.netcdf3
### Author: Jeff Whitaker
import tables.netcdf3 as NetCDF
import time
history = 'Created ' + time.ctime(time.time())
file = NetCDF.NetCDFFile('test.h5', 'w', history=history)
file.createDimension('level', 12)
file.createDimension('time', None)
file.createDimension('lat', 90)
print '**dimensions**'
print file.dimensions
times = file.createVariable('time', 'd', ('time', ))
levels = file.createVariable('level', 'i', ('level', ))
latitudes = file.createVariable('latitude', 'f', ('lat', ))
temp = file.createVariable('temp', 'f', (
'time',
'level',
'lat',
))
# try this to see how much smaller the file gets.
#temp = file.createVariable('temp','f',('time','level','lat',),least_significant_digit=1)
pressure = file.createVariable('pressure', 'i', (
'level',
'lat',
))
print '**variables**'
print file.variables